[GenABEL-dev] export.plink bug: should we change the default?

[Yurii Aulchenko]

Hi Maria,

if my understanding is correct, the fix is now only in the devel-version on
SVN - so you would need to export and build package if you really want it
(see http://genabel.r-forge.r-project.org/tutHowToInstallDevelVersion.html).

But the 'fix' is very simple (and is not actually fixing anything - just
trying to avoid confusion!): the default option now is set to
'transpose=TRUE'. So you can simply set this up manually when calling
'export.plink' :)

Yurii


On Wed, Apr 3, 2013 at 11:58 AM, Maria G <mgmaria at yandex.ru> wrote:

> Dear Lennart,
>
> that's really helpful, thank you!
>
> Does it mean I have to update the version of GenABEL to get read of the
> bug? Which version is fine?
>
>
> best
> Mariya
>
> 02.04.2013, 20:30, "L.C. Karssen" <lennart at karssen.org>:
> > Dear list,
> >
> > As I didn't get any comments to dissuade me, I've just committed a
> > change that sets the default behaviour of export.plink() in GenABEL to
> > export .tped/.tfam files. This works around bug #2055.
> >
> > Best,
> >
> > Lennart.
> >
> > On 28/03/13 14:34, L.C. Karssen wrote:
> >
> >>  Dear list,
> >>
> >>  We recently got bitten by bug #2055 (ref [1]) in GenABEL's
> >>  export.plink() again. Data was exported to .ped format and everything
> >>  seemed to have gone well, however, we later found out that the exported
> >>  genotypes were wrong. Exporting to .tped (export.plink(...,
> >>  transpose=TRUE)) worked fine.
> >>
> >>  I think we should change the default for the transpose option to TRUE
> >>  and add a warning in case someone sets it to FALSE. I'm of course
> >>  willing to write the necessary code.
> >>  At least this will safeguard the users from this problem until the
> >>  actual bug is fixed.
> >>
> >>  What are you're thoughts on this?
> >>
> >>  Best,
> >>
> >>  Lennart.
> >>
> >>  [1]
> >>
> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=2055&group_id=505&atid=2058
> >>  --
> >>  -----------------------------------------------------------------
> >>  L.C. Karssen
> >>  Utrecht
> >>  The Netherlands
> >>
> >>  lennart at karssen.org
> >>  http://blog.karssen.org
> >>
> >>  Stuur mij aub geen Word of Powerpoint bestanden!
> >>  Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> >>  ------------------------------------------------------------------
> >>
> >>  _______________________________________________
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> >>  genabel-devel at lists.r-forge.r-project.org
> >>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >
> > --
> > -----------------------------------------------------------------
> > L.C. Karssen
> > Utrecht
> > The Netherlands
> >
> > lennart at karssen.org
> > http://blog.karssen.org
> >
> > Stuur mij aub geen Word of Powerpoint bestanden!
> > Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> > ------------------------------------------------------------------
> >
> > ,
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> >
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